As you exit ontop Mossdeep City, you'll suddenly feel the ground shake violently; to the south, you can see a bright viridian beam shoot up into the sky from around Route 128. Take particular note of the area shown during the cutscene; you'll go there eventually.
Steven will take you to his place and explain what's going on: that, apparently, the ancient Pokémon hidden beneath Route 128 has been unsealed by Team Aqua/Magma. He'll give you HM07 (Dive) to help you on your way. You'll also get the Devon Scuba Gear to allow you to be underwater.
With that done, it's time to leave. Go south onto Route 127 .